Alu-mediated detection of DNA damage in the human genome

Quantification of Double Stranded DNA Breaks and Telomere Length as Proxies for Corneal Damage and Replicative Stress in Human Keratoconus Corneas

Purpose

The pathogenesis of keratoconus (KC) is multifactorial, and associated with oxidative stress and subsequent DNA damage. We investigate differences in DNA damage and replicative stress in patients with KC, and in healthy and diseased controls.

Methods

We obtained 64 corneal buttons from 27 patients with KC after corneal transplant surgery, 21 with a decompensated graft (DG), and 16 healthy controls (HC). The amount of intact Alu elements per genome copy as measured by quantitative polymerase chain reaction (qPCR) was used to quantify intact DNA. Telomere length was measured as a proxy for replicative stress. In addition, telomerase reverse transcriptase (hTERT) gene expression level was assessed.

Results

Mean (± standard deviation [SD]) DNA damage was similar between the KC (5.56 ± 14.08), DG (3.16 ± 8.22), and HC (3.51 ± 6.66) groups (P = 0.807). No associations were found between DNA damage and patient age (P = 0.523), atopic constitution (P = 0.240), or contact lens wear (P = 0.393). Telomere length differed (P = 0.034), most notably in the KC group, and hTERT was not detected in any corneal sample. Three cross-linked (CXL) KC corneas did not contain significantly more DNA damage (×2.6, P = 0.750).

Conclusions

Based on these findings, differences in actual corneal DNA damage in KC could not be identified, and the longer telomere length in KC did not support replicative stress as a major etiologic factor in the pathogenesis of KC. Future longitudinal investigations on KC etiology should assess progressively early cases to better comprehend the cellular and molecular processes preceding the archetypical morphologic changes.

Translational Relevance

The standard treatment for progressive keratoconus promotes the crosslinking of collagen fibers through ultraviolet radiation and the subsequent formation of reactive oxygen species. Our study helps to underline the safety of this treatment approach.

Reflections on Basic Science Studies Involving Low Doses of Ionizing Radiation

Investigation of health effects of low doses of radiation as a field of study has been riddled with difficulties since its inception. In this document we will use 100 mGy as the cutoff upper limit for low-dose radiation, borrowing this definition from the U.S. Department of Energy, although other agencies and researchers sometimes include up to five-fold higher doses under the same title. Difficulties in this area of research are most often ascribed to the fact that effects of low doses of radiation are subtle and difficult to distinguish from the plethora of other low-grade stresses. Thus, for example, most epidemiological studies include hundreds of thousands of samples and generate risk estimates that are statistically meaningful only when they are considered on a scale of hundreds or thousands of people. A logical approach to remedy the situation for low-dose research was to conduct well-controlled animal studies with hundreds of animals; nevertheless, even after many such studies were completed, our understanding of the biological basis for risk from low-dose radiation exposure is still not conclusive. In this paper we argue that the problem lies in the fact that our approach to animal studies is not comprehensive but conceptually binary. While some researchers apply epidemiological models to animal data, others look into molecular and cellular biology only. Very few studies are conducted to bridge this gap and consider how a realistic model of DNA damage could be integrated into a realistic model of radiation carcinogenesis.

MMSET/WHSC1 enhances DNA damage repair leading to an increase in resistance to chemotherapeutic agents

MMSET/WHSC1 is a histone methyltransferase (HMT) overexpressed in t(4;14)+ multiple myeloma (MM) patients, believed to be the driving factor in the pathogenesis of this MM subtype. MMSET overexpression in MM leads to an increase in histone 3 lysine 36 dimethylation (H3K36me2), and a decrease in histone 3 lysine 27 trimethylation (H3K27me3), as well as changes in proliferation, gene expression, and chromatin accessibility. Prior work linked methylation of histones to the ability of cells to undergo DNA damage repair. In addition, t(4;14)+ patients frequently relapse after regimens that include DNA damage-inducing agents, suggesting that MMSET may play a role in DNA damage repair and response. In U2OS cells, we found that MMSET is required for efficient non-homologous end joining as well as homologous recombination. Loss of MMSET led to loss of expression of several DNA repair proteins, as well as decreased recruitment of DNA repair proteins to sites of DNA double strand breaks (DSBs). Using genetically matched MM cell lines that had either high (pathological) or low (physiological) expression of MMSET, we found that MMSET high cells had increased damage at baseline. Upon addition of a DNA damaging agent, MMSET high cells repaired DNA damage at an enhanced rate and continued to proliferate, whereas MMSET low cells accumulated DNA damage and entered cell cycle arrest. In a murine xenograft model using t(4;14)+ KMS11 MM cells harboring an inducible MMSET shRNA, depletion of MMSET enhanced the efficacy of chemotherapy, inhibiting tumor growth and extending survival. These findings help explain the poorer prognosis of t(4;14) MM and further validate MMSET as a potential therapeutic target in MM and other cancers.

High-resolution characterization of CPD hotspot formation in human fibroblasts

Repair of DNA lesions must occur within the chromatin landscape and is associated with alterations in histone modifications and nucleosome rearrangement. To directly associate these chromatin features with DNA damage and repair, it is necessary to be able to map DNA adducts. We have developed a cyclobutane pyrimidine dimer (CPD)-specific immunoprecipitation method and mapped ultraviolet damage hotspots across human chromosomes 1 and 6. CPD hotspots occur almost equally in genic and intergenic regions. However, these hotspots are significantly more prevalent adjacent to repeat elements, especially Alu repeats. Nucleosome mapping studies indicate that nucleosomes are consistently positioned at Alu elements where CPD hotspots form, but by 2 h post-irradiation, these same regions are significantly depleted of nucleosomes. These results indicate that nucleosomes associated with hotspots of CPD formation are readily rearranged, potentially making them accessible to DNA repair machinery. Our results represent the first chromosome scale map of ultraviolet-induced DNA lesions in the human genome, and reveal the sequence features and dynamic chromatin changes associated with CPD hotspots.

Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs

For many years, Taq polymerase has served as the stalwart enzyme in the PCR amplification of DNA. However, a major limitation of Taq is its inability to amplify damaged DNA, thereby restricting its usefulness in forensic applications. In contrast, Y-family DNA polymerases, such as Dpo4 from Sulfolobus solfataricus, can traverse a wide variety of DNA lesions. Here, we report the identification and characterization of five novel thermostable Dpo4-like enzymes from Acidianus infernus, Sulfolobus shibatae, Sulfolobus tengchongensis, Stygiolobus azoricus and Sulfurisphaera ohwakuensis, as well as two recombinant chimeras that have enhanced enzymatic properties compared with the naturally occurring polymerases. The Dpo4-like polymerases are moderately processive, can substitute for Taq in PCR and can bypass DNA lesions that normally block Taq. Such properties make the Dpo4-like enzymes ideally suited for the PCR amplification of damaged DNA samples. Indeed, by using a blend of Taq and Dpo4-like enzymes, we obtained a PCR amplicon from ultraviolet-irradiated DNA that was largely unamplifyable with Taq alone. The inclusion of thermostable Dpo4-like polymerases in PCRs, therefore, augments the recovery and analysis of lesion-containing DNA samples, such as those commonly found in forensic or ancient DNA molecular applications.

Differential expression of B1-containing transcripts in Leishmania-exposed macrophages

When the parasitic protozoan Leishmania infect host macrophage cells, establishment of the infection requires alteration in the expression of genes in both the parasite and the host cells. In the early phase of infection of macrophages in vitro, Leishmania exposure affects the expression of a group of mouse macrophage genes containing the repetitive transposable element designated B1 sequence. In Leishmania-exposed macrophages compared with unexposed macrophages, small (approximately 0.5 kilobase) B1-containing RNAs (small B1-RNAs) are down-regulated, and large (1-4 kilobases) B1-containing RNAs (large B1-RNA) are up-regulated. The down-regulation of small B1-RNAs precedes the up-regulation of large B1-RNAs in Leishmania-exposed macrophages. These differential B1-containing gene expressions in Leishmania-exposed macrophages were verified using individual small-B1-RNA and large B1-RNA. The differential expressions of the B1-containing RNAs at the early phase of Leishmania-macrophage interaction may associate the establishment of the leishmanial infection.

Mitochondrial DNA damage and a hypoxic response are induced by CoCl(2) in rat neuronal PC12 cells

Generation of reactive oxygen species (ROS) and activation of a transcriptional program that mimics the hypoxic response have been documented in cultured cells in the presence of cobalt chloride. We found that in the presence of hypoxia-mimicking concentrations of CoCl(2), mitochondrial but not nuclear DNA damage is induced in rat neuronal, PC12 cells. To our knowledge, this is the first documentation of induction of mitochondrial DNA (mtDNA) damage under these conditions. Likewise, we provide the first evidence for elevation of MYH, the mammalian homolog of the Escherichia coli MutY DNA glycosylase, in mammalian cells. Recently, the human MYH was implicated in repair of oxidative DNA damage and shown to carry a mitochondrial localization sequence. Here, an induction of mtDNA damage and a time-dependent increase in the MYH level were detected with exposure of cells to 100 microM CoCl(2). In addition, the levels of proteins involved in cellular responses to hypoxia, ROS and nuclear DNA damage; hypoxia-inducible factor 1alpha(HIF-1alpha), p53, p21 and PCNA were also modulated temporally. Earlier studies suggested that the mtDNA is a primary target for oxidative damage. Our findings extend these observations and suggest that activation of DNA repair processes is associated with the presence of mtDNA damage.

Rapid SINE-mediated detection of cisplatin:DNA adduct formation in vitro and in vivo in blood

Cisplatin (cis-dichlorodiammine platinum II) is one of the most effective antitumor agents to date. Its usefulness is limited, however, by toxicity to healthy tissues, most notably, its nephrotoxicity. To maximize the chemotherapeutic potential of cisplatin and minimize its adverse effects, it is imperative to monitor formation of cisplatin:DNA adducts throughout treatment. We developed a novel, highly sensitive, SINE (Short Interspersed DNA Element)-mediated. PCR-based assay for detection of cisplatin adducts in vitro and in vivo, in DNA from mouse blood cells. The assay relies on the abundance, dispersion and conservation of SINEs in mammalian genomes. The B1 elements at a copy number of 50,000-80,000 are the most abundant SINEs in the mouse genome. Due to their strong sequence conservation, primers complementary to the B1 consensus sequence anneal to the majority of their targets in the genome and allow simultaneous amplification of long random segments of genomic DNA. Thus, in conjunction with the fact that cisplatin adducts block the progression of thermostable polymerase, B1 element-anchored PCR makes a sensitive tool for assessing the overall integrity of the transcribed regions in the mouse genome. The high sensitivity of the assay allows detection of DNA damage at the low cisplatin dosage of 1-8 mg/kg that is considered as sub-chemotherapeutic in experimental animal models. The sensitivity range therefore, makes this assay suitable for the development of predictive correlation for both, the efficacy of treatment as well as induction of nephrotoxicity.